A Quantitative Comparison of Cell-Type-Specific Microarray Gene Expression Profiling Methods in the Mouse Brain (original) (raw)
Figure 4
Gene expression profiles of Purkinje cells purified by three different methods show striking differences.
(A) Scatter plot depicting the maximum fold difference of expression level between methods (vertical axis) and the corresponding ANOVA p-value (horizontal axis) for all genes (where an ANOVA was performed for each gene across groups defined by purification method). Upper right quadrant formed by the two intersecting red lines delineates significantly differentially expressed genes (maximum fold difference >2, ANOVA p-value < 1e-3). (**B**) Heat map depicting the most significantly differentially expressed genes (maximum fold difference between methods >20, ANOVA p-value < 1e-10) where each column represents an individual replicate sample. Gene names given in red font indicate genes that have a strong likelihood of being non-Purkinje gene contaminants (based on Allen Brain Atlas In-situ data and literature searches, see Results), green font indicates non-translated mRNAs, and the expression specificity of the remaining genes is unknown. (C) Pie graphs depicting the percentage of method enriched and depleted genes that are also enriched in glia, and thus are likely to be the result of contamination. The total number of genes in each category is given beneath each graph. (D) Gene ontology terms associated with Manual and LCM enriched genes and TRAP depleted genes. Number of genes associated with each term is given on the vertical axis.